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- PDB-8e1h: Asp1 kinase in complex with ADP Mg 5-IP7 -

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Basic information

Entry
Database: PDB / ID: 8e1h
TitleAsp1 kinase in complex with ADP Mg 5-IP7
ComponentsInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase
KeywordsTRANSFERASE
Function / homology
Function and homology information


regulation of bipolar cell growth / inositol-1-diphosphate-2,3,4,5,6-pentakisphosphate diphosphatase activity / inositol-1,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 1-diphosphatase activity / regulation of mitotic spindle elongation (spindle phase three) / Synthesis of pyrophosphates in the cytosol / diphosphoinositol-pentakisphosphate 1-kinase / inositol heptakisphosphate kinase activity / diphosphoinositol-pentakisphosphate kinase activity / inositol hexakisphosphate 1-kinase activity / inositol hexakisphosphate 3-kinase activity ...regulation of bipolar cell growth / inositol-1-diphosphate-2,3,4,5,6-pentakisphosphate diphosphatase activity / inositol-1,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 1-diphosphatase activity / regulation of mitotic spindle elongation (spindle phase three) / Synthesis of pyrophosphates in the cytosol / diphosphoinositol-pentakisphosphate 1-kinase / inositol heptakisphosphate kinase activity / diphosphoinositol-pentakisphosphate kinase activity / inositol hexakisphosphate 1-kinase activity / inositol hexakisphosphate 3-kinase activity / inositol-1,3,4,5,6-pentakisphosphate kinase activity / inositol hexakisphosphate kinase activity / inositol hexakisphosphate 5-kinase activity / inositol phosphate metabolic process / signaling / inositol phosphate biosynthetic process / inositol metabolic process / mitotic spindle assembly / regulation of microtubule cytoskeleton organization / 2 iron, 2 sulfur cluster binding / cytoskeleton / phosphorylation / ATP hydrolysis activity / ATP binding / nucleus / cytosol
Similarity search - Function
Histidine acid phosphatase, VIP1 family / VIP1, N-terminal / Diphosphoinositol pentakisphosphate kinase 2 N-terminal domain / ATP-grasp fold, RimK-type / RimK-like ATP-grasp domain / Histidine phosphatase superfamily, clade-2 / Histidine phosphatase superfamily (branch 2) / Histidine phosphatase superfamily
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Chem-I7P / Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGoldgur, Y. / Shuman, S. / Benjamin, B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM126945 United States
CitationJournal: Mbio / Year: 2022
Title: Structures of Fission Yeast Inositol Pyrophosphate Kinase Asp1 in Ligand-Free, Substrate-Bound, and Product-Bound States.
Authors: Benjamin, B. / Goldgur, Y. / Jork, N. / Jessen, H.J. / Schwer, B. / Shuman, S.
History
DepositionAug 10, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 4, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase
B: Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9567
Polymers76,7162
Non-polymers1,2405
Water7,494416
1
A: Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5986
Polymers38,3581
Non-polymers1,2405
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase


Theoretical massNumber of molelcules
Total (without water)38,3581
Polymers38,3581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.600, 87.123, 86.025
Angle α, β, γ (deg.)90.000, 94.730, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase / Cortical actin cytoskeleton protein asp1 / InsP6 and PP-IP5 kinase


Mass: 38357.867 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972 / ATCC 24843 / Gene: asp1, vip1, SPCC1672.06c / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O74429, diphosphoinositol-pentakisphosphate 1-kinase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-I7P / (1r,2R,3S,4s,5R,6S)-2,3,4,5,6-pentakis(phosphonooxy)cyclohexyl trihydrogen diphosphate / 1D-myo-inositol 5-diphosphate 1,2,3,4,6-pentakisphosphate


Mass: 740.015 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H19O27P7 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 416 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M bis-tris propane (pH 8.1), 0.15 M NaF, and 20% PEG 3,350
Temp details: ambient

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 52215 / % possible obs: 95.2 % / Redundancy: 2.9 % / Biso Wilson estimate: 31.12 Å2 / CC1/2: 0.994 / Rpim(I) all: 0.052 / Net I/σ(I): 31.3
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 2.6 % / Num. unique obs: 2618 / CC1/2: 0.804 / Rpim(I) all: 0.346 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NZM

4nzm


Resolution: 1.9→47.44 Å / SU ML: 0.2444 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.4369
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.234 2012 3.86 %
Rwork0.1965 50148 -
obs0.198 52160 94.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.71 Å2
Refinement stepCycle: LAST / Resolution: 1.9→47.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5198 0 70 416 5684
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00775378
X-RAY DIFFRACTIONf_angle_d1.06657282
X-RAY DIFFRACTIONf_chiral_restr0.0639784
X-RAY DIFFRACTIONf_plane_restr0.0076937
X-RAY DIFFRACTIONf_dihedral_angle_d11.9638730
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.32061530.28353293X-RAY DIFFRACTION88.02
1.95-20.2971380.25493686X-RAY DIFFRACTION97.73
2-2.060.27911420.25043710X-RAY DIFFRACTION97.74
2.06-2.120.31731470.24653679X-RAY DIFFRACTION97.13
2.12-2.20.3091480.22813596X-RAY DIFFRACTION95.83
2.2-2.290.27411480.21563675X-RAY DIFFRACTION97.63
2.29-2.390.21431470.21933714X-RAY DIFFRACTION97.25
2.39-2.520.23921370.21613617X-RAY DIFFRACTION96.31
2.52-2.680.24581480.21943642X-RAY DIFFRACTION95.68
2.68-2.880.26481330.21253531X-RAY DIFFRACTION93.33
2.88-3.170.24471400.20553409X-RAY DIFFRACTION89.42
3.17-3.630.21761450.18123411X-RAY DIFFRACTION90.07
3.63-4.580.19121390.15923481X-RAY DIFFRACTION91.34
4.58-47.440.21281470.17493704X-RAY DIFFRACTION95.35
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.06210990596-0.535557519825-0.8616912326361.192315323180.2140402691081.0076520364-0.1019423564330.0198762556428-0.163667672883-0.01809702564660.101082172378-0.2380163072160.2031602406910.0986024442631-4.15471526344E-50.3694252979260.03551599260080.01831556816830.2903162721730.02526987071370.35277032047119.7348590176-26.82197476513.09117408562
20.2126912446630.101205424281-0.1001209261191.07330718660.2090277791761.149045802090.0349712980968-0.0411036925022-0.00530359513041-0.05677436297760.00312679855271-0.0178662492151-0.104611133538-0.01730287150121.55420215433E-50.272322824820.0387434003980.007684031949930.266882133960.01150280873540.2501294107398.26258209377-3.9686622533415.8999234343
30.829360741060.267698919227-0.5776093454331.089809499890.5048064868511.193763652020.008221849105280.0317733300118-0.0168481854165-0.167227445348-0.06530622465590.00307559292040.00721302271239-0.2688736691030.0003294942744560.347383298890.0227015816003-0.01540220671020.3055007609710.02587020922670.2546112726942.5268368577-20.16122311386.53939283482
40.98976571823-0.418649844009-0.09471120783731.509878945470.09523502497240.938468179631-0.04118342900460.171547831430.240252815507-0.1808168107420.0305668658440.0691684574113-0.365056892555-0.03581431526430.0001099114713680.421975511069-0.025072727478-0.01965550853410.2865520285510.009778828182080.33744778517924.9774776367-22.261832944635.8074388914
5-0.127284705291-0.224777530061-0.1603036933170.280666069550.310835132216-0.0145925988486-0.0097353125974-0.055160107215-0.1682162459280.152290919283-0.00309227111577-0.02748339499720.161466459436-0.0677914385519-0.0001136969249450.249191704894-0.0264813700105-0.0221507000290.291558110686-0.004946021513230.28581379303334.6476349496-29.018054883642.8731033406
60.318666376012-0.746645773317-0.4342650266770.2341789004810.2379714133070.755257286134-0.0108152079093-0.16020749488-0.1169212776720.08751734881990.0424729541484-0.0356404253424-0.1713952816740.225174867584-3.23629911292E-50.257052825795-0.03051301917570.006409556916060.284146481004-0.00753520938460.2597884700942.7684209704-45.63508348339.457315398
71.145925243970.3938524962250.007197810405831.0757566338-0.329797081821.27149850691-0.02370609206880.00326973421123-0.046065436855-0.1469614995130.110526011723-0.0307881834703-0.1042778400560.08981843356382.71429350124E-50.2515310677070.00789291255958-0.01864144866350.24178247162-0.025910824160.23143300315147.7758444992-48.873240102221.5791878527
80.395583941449-0.420998997654-0.1392831093961.07525794235-0.148332351640.338855208583-0.1451067756720.126807794159-0.161735078498-0.1883754258330.01161659810330.0693907885650.0867908732239-0.0450527569445-1.2207392878E-50.227524394689-0.0274330730937-0.01078211915080.289545552668-0.04139780286820.23524743339440.1719568633-48.810663625720.270500105
90.6327713673740.05813760786840.1897231751750.2819111468550.1059386599960.1080139380150.2300057774610.1808799058250.16035375315-0.2046127150760.0720259615226-0.214556677848-0.188124098646-0.222557042994-0.0002585083808940.3737587763740.0139343057534-0.003590896843940.378953422531-0.01756566311190.35841469359219.0929084887-46.504533486325.74456331
101.397237204680.126312127248-0.1859668981270.9586113589710.2232814793420.525205778771-0.05267533315780.00492709537242-0.05954145516490.100444875297-0.009788234091070.09437120592080.04991056411-0.02120445814635.3401723959E-50.231514334798-0.0223493942442-0.006153836669930.271802445377-0.01284003315540.27821641100622.9964845326-42.046589341634.341546649
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 31 through 122 )AA31 - 1221 - 92
22chain 'A' and (resid 123 through 299 )AA123 - 29993 - 269
33chain 'A' and (resid 300 through 362 )AA300 - 362270 - 332
44chain 'B' and (resid 33 through 95 )BB33 - 951 - 63
55chain 'B' and (resid 96 through 122 )BB96 - 12264 - 90
66chain 'B' and (resid 123 through 163 )BB123 - 16391 - 131
77chain 'B' and (resid 164 through 230 )BB164 - 230132 - 198
88chain 'B' and (resid 231 through 264 )BB231 - 264199 - 232
99chain 'B' and (resid 265 through 299 )BB265 - 299233 - 252
1010chain 'B' and (resid 300 through 362 )BB300 - 362253 - 315

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